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mmu_circSos1_297
Basic information of circular RNA
PanCircBase ID:
mmu_circSos1_297
mm39_Chr. Position ID:
chr17|80761184|80762612|-
Gene name:
Sos1
Transcript:
ENSMUST00000068714.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,1296
Genomic length:
1428
Exon/intron sizes in nt:
1,65,132
Flanking exon/introns:
chr17:80759619-80761184|chr17:80762612-80767350
Splice length:
297
Other database IDs:
circBase: hsa_circ_0119992, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_41225
Human Ortholog IDs:
Mature spliced Sequence:
GAACGTGTTCAAAAGAGTTTTCCTCATCCAATTGATAAGTGGGCAATAGCTGATGCCCAATCAGCCATTGAAAAGAGGAAGAGACGAAATCCTTTATCGCTGCCAGCAGAAAGAATTCATCATTTATTAAGGGAGGTCCTCGGTTATAAAATTGACCACCAGGTTTCTGTTTACATAGTAGCAGTATTAGAATACATTTCTGCAGATATTTTAAAGCTCGTGGGGAATTATGTAAGAAATATACGGCATTATGAAATTACAAAACAAGACATTAAAGTGGCAATGTGTGCTGATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCTCGTGGGGAATTATGT
56.9
GCATCAGCTATTGCCCACTT
58.6
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCTCGTGGGGAATTATGT
56.9
TTTCAATGGCTGATTGGGCA
58.36
157
PCR template sequence:
TTCTGCAGATATTTTAAAGCTCGTGGGGAATTATGTAAGAAATATACGGCATTATGAAATTACAAAACAAGACATTAAAGTGGCAATGTGTGCTGATAAGGAACGTGTTCAAAAGAGTTTTCCTCATCCAATTGATAAGTGGGCAATAGCTGATGCCCAATCAGCCATTGAAAAGAGGAAGAGACGAAATCCTTTATCGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGTGCTGATAAGGAACGTGTTCAAA
siRNA sets
TTTGAACACGTTCCTTATC, TTGAACACGTTCCTTATCA, GAACACGTTCCTTATCAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSOS1_297_ORF_1
0.9722
-0.055552936
0.193927998
312
ORF sequence:
ATGTGTGCTGATAAGGAACGTGTTCAAAAGAGTTTTCCTCATCCAATTGATAAGTGGGCAATAGCTGATGCCCAATCAGCCATTGAAAAGAGGAAGAGACGAAATCCTTTATCGCTGCCAGCAGAAAGAATTCATCATTTATTAAGGGAGGTCCTCGGTTATAAAATTGACCACCAGGTTTCTGTTTACATAGTAGCAGTATTAGAATACATTTCTGCAGATATTTTAAAGCTCGTGGGGAATTATGTAAGAAATATACGGCATTATGAAATTACAAAACAAGACATTAAAGTGGCAATGTGTGCTGATAAG
Peptide sequence:
MCADKERVQKSFPHPIDKWAIADAQSAIEKRKRRNPLSLPAERIHHLLREVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCADK
IRESfinder result
IRESfinder score
0.673452063
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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